Molecular dynamics simulations of DPPC bilayers using "LIME", a new coarse-grained model

J Phys Chem B. 2013 May 2;117(17):5019-30. doi: 10.1021/jp309712b. Epub 2013 Apr 16.

Abstract

A new intermediate resolution model for phospholipids, LIME, designed for use with discontinuous molecular dynamics (DMD) simulations is presented. The implicit-solvent model was developed using a multiscale modeling approach in which the geometric and energetic parameters are obtained by collecting data from atomistic simulations of a system composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) molecules and explicit water. In the model, 14 coarse-grained sites that are classified as 1 of 6 types represent DPPC. DMD simulations performed on a random solution of DPPC resulted in the formation of a defect-free bilayer in less than 4 h. The bilayer formed quantitatively reproduces the main structural properties (e.g., area per lipid, bilayer thickness, bond order parameters) that are observed experimentally. In addition, the bilayer transitions from a liquid-crystalline phase to a tilted gel phase when the temperature is reduced. Transbilayer movement of a lipid from the bottom leaflet to the top leaflet is observed when the temperature is increased.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • 1,2-Dipalmitoylphosphatidylcholine / chemistry*
  • Lipid Bilayers / chemistry*
  • Molecular Dynamics Simulation*
  • Monte Carlo Method
  • Temperature
  • Thermodynamics
  • Water / chemistry

Substances

  • Lipid Bilayers
  • Water
  • 1,2-Dipalmitoylphosphatidylcholine